AMBER Archive (2004)

Subject: AMBER: B factors from simulation and from cryst

From: Vlad Cojocaru (
Date: Mon Jan 26 2004 - 10:21:50 CST

Dear Amber comunity,
    I have a question regarding the B factors:
Should one expect the B factors calculated from the simulation to match
exactly the B factors from the X-Ray structure? If not could somebody
explain what to expect in general?

In my case I a simulating a protein-rna complex and in general the B
factors for the protein atoms calculated from the simulation are smaller
comparing to the ones from the crystal structure except the N and C
terminus where they are bigger? Would that be a concern for the
simulation's quality?
Thank you very much for any replies
Best wishes

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  

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